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  1. Project Clover database Thu Nov 28 2024 18:06:40 GMT
  2. Package jalview.ext.pymol

File PymolCommandsTest.java

 

Code metrics

0
136
19
1
353
276
19
0.14
7.16
19
1

Classes

Class Line # Actions
PymolCommandsTest 41 136 19
1.0100%
 

Contributing tests

This file is covered by 18 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.ext.pymol;
22   
23    import static org.testng.Assert.assertEquals;
24    import static org.testng.Assert.assertTrue;
25   
26    import java.awt.Color;
27    import java.util.HashMap;
28    import java.util.LinkedHashMap;
29    import java.util.List;
30    import java.util.Map;
31   
32    import org.testng.annotations.BeforeClass;
33    import org.testng.annotations.Test;
34   
35    import jalview.ext.rbvi.chimera.ChimeraCommands;
36    import jalview.structure.AtomSpecModel;
37    import jalview.structure.StructureCommand;
38    import jalview.structure.StructureCommandI;
39    import jalview.structure.StructureCommandsI.AtomSpecType;
40   
 
41    public class PymolCommandsTest
42    {
43    private PymolCommands testee;
44   
 
45  1 toggle @BeforeClass(alwaysRun = true)
46    public void setUp()
47    {
48  1 testee = new PymolCommands();
49    }
50   
 
51  1 toggle @Test(groups = { "Functional" })
52    public void testColourBySequence()
53    {
54   
55  1 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
56  1 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 2, 5, "A");
57  1 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 7, 7, "B");
58  1 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 9, 23, "A");
59  1 PymolCommands.addAtomSpecRange(map, Color.blue, "1", 1, 1, "A");
60  1 PymolCommands.addAtomSpecRange(map, Color.blue, "1", 4, 7, "B");
61  1 PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 8, 8, "A");
62  1 PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 3, 5, "A");
63  1 PymolCommands.addAtomSpecRange(map, Color.red, "0", 3, 5, "A");
64  1 PymolCommands.addAtomSpecRange(map, Color.red, "0", 6, 9, "A");
65   
66    // Colours should appear in the Pymol command in the order in which
67    // they were added; within colour, by model, by chain, ranges in start order
68  1 List<StructureCommandI> commands = testee.colourBySequence(map);
69  1 assertEquals(commands.size(), 3);
70  1 assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
71    "0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
72  1 assertEquals(commands.get(1),
73    new StructureCommand("color", "0xffff00", "1//A/3-5+8/"));
74  1 assertEquals(commands.get(2),
75    new StructureCommand("color", "0xff0000", "0//A/3-9/"));
76    }
77   
 
78  1 toggle @Test(groups = "Functional")
79    public void testGetAtomSpec()
80    {
81  1 AtomSpecModel model = new AtomSpecModel();
82  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
83  1 model.addRange("1", 2, 4, "A");
84  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
85    "1//A/2-4/");
86  1 model.addRange("1", 8, 8, "A");
87  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
88    "1//A/2-4+8/");
89  1 model.addRange("1", 5, 7, "B");
90  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
91    "1//A/2-4+8/ 1//B/5-7/");
92  1 model.addRange("1", 3, 5, "A");
93  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
94    "1//A/2-5+8/ 1//B/5-7/");
95  1 model.addRange("0", 1, 4, "B");
96  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
97    "0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
98  1 model.addRange("0", 5, 9, "C");
99  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
100    "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
101  1 model.addRange("1", 8, 10, "B");
102  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
103    "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
104  1 model.addRange("1", 8, 9, "B");
105  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
106    "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
107  1 model.addRange("0", 3, 10, "C"); // subsumes 5-9
108  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
109    "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
110  1 model.addRange("5", 25, 35, " ");
111  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
112    "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
113   
114    }
115   
 
116  1 toggle @Test(groups = { "Functional" })
117    public void testSuperposeStructures()
118    {
119  1 AtomSpecModel ref = new AtomSpecModel();
120  1 ref.addRange("1", 12, 14, "A");
121  1 ref.addRange("1", 18, 18, "B");
122  1 ref.addRange("1", 22, 23, "B");
123  1 AtomSpecModel toAlign = new AtomSpecModel();
124  1 toAlign.addRange("2", 15, 17, "B");
125  1 toAlign.addRange("2", 20, 21, "B");
126  1 toAlign.addRange("2", 22, 22, "C");
127  1 List<StructureCommandI> commands = testee.superposeStructures(ref,
128    toAlign, AtomSpecType.ALPHA);
129  1 assertEquals(commands.size(), 4);
130  1 String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
131  1 String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
132  1 String refSpec = "1//A/12-14/ 1//B/18+22-23/";
133  1 String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
134  1 String altLoc = " and (altloc '' or altloc 'a'))";
135    // super command: separate arguments for regions to align
136  1 assertEquals(commands.get(1), new StructureCommand("pair_fit",
137    toAlignSpecCA + altLoc, refSpecCA + altLoc));
138    // show aligned regions: one argument for combined atom specs
139  1 assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
140    refSpec + " " + toAlignSpec));
141    }
142   
 
143  1 toggle @Test(groups = "Functional")
144    public void testGetAtomSpec_alphaOnly()
145    {
146  1 AtomSpecModel model = new AtomSpecModel();
147  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
148  1 model.addRange("1", 2, 4, "A");
149  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
150    "1//A/2-4/CA");
151  1 model.addRange("1", 8, 8, "A");
152  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
153    "1//A/2-4+8/CA");
154  1 model.addRange("1", 5, 7, "B");
155  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
156    "1//A/2-4+8/CA 1//B/5-7/CA");
157  1 model.addRange("1", 3, 5, "A");
158  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
159    "1//A/2-5+8/CA 1//B/5-7/CA");
160  1 model.addRange("0", 1, 4, "B");
161  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
162    "0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
163  1 model.addRange("0", 5, 9, "C");
164  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
165    "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
166  1 model.addRange("1", 8, 10, "B");
167  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
168    "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
169  1 model.addRange("1", 8, 9, "B");
170  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
171    "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
172  1 model.addRange("0", 3, 10, "C"); // subsumes 5-9
173  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
174    "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
175  1 model.addRange("5", 25, 35, " ");
176  1 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
177    "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA");
178    }
179   
 
180  1 toggle @Test(groups = "Functional")
181    public void testGetModelStartNo()
182    {
183  1 assertEquals(testee.getModelStartNo(), 0);
184    }
185   
 
186  1 toggle @Test(groups = "Functional")
187    public void testGetResidueSpec()
188    {
189  1 assertEquals(testee.getResidueSpec("ALA"), "resn ALA");
190    }
191   
 
192  1 toggle @Test(groups = "Functional")
193    public void testShowBackbone()
194    {
195  1 List<StructureCommandI> cmds = testee.showBackbone();
196  1 assertEquals(cmds.size(), 2);
197  1 assertEquals(cmds.get(0), new StructureCommand("hide", "everything"));
198  1 assertEquals(cmds.get(1), new StructureCommand("show", "ribbon"));
199    }
200   
 
201  1 toggle @Test(groups = "Functional")
202    public void testColourByCharge()
203    {
204  1 List<StructureCommandI> cmds = testee.colourByCharge();
205  1 assertEquals(cmds.size(), 4);
206  1 assertEquals(cmds.get(0), new StructureCommand("color", "white", "*"));
207  1 assertEquals(cmds.get(1),
208    new StructureCommand("color", "red", "resn ASP resn GLU"));
209  1 assertEquals(cmds.get(2),
210    new StructureCommand("color", "blue", "resn LYS resn ARG"));
211  1 assertEquals(cmds.get(3),
212    new StructureCommand("color", "yellow", "resn CYS"));
213    }
214   
 
215  1 toggle @Test(groups = "Functional")
216    public void testOpenCommandFile()
217    {
218  1 assertEquals(testee.openCommandFile("commands.pml"),
219    new StructureCommand("run", "commands.pml"));
220    }
221   
 
222  1 toggle @Test(groups = "Functional")
223    public void testSaveSession()
224    {
225  1 assertEquals(testee.saveSession("somewhere.pse"),
226    new StructureCommand("save", "somewhere.pse"));
227    }
228   
 
229  1 toggle @Test(groups = "Functional")
230    public void testOpenSession()
231    {
232  1 assertEquals(testee.openSession("/some/path"),
233    new StructureCommand("load", "/some/path", "", "0", "pse"));
234    }
235   
 
236  1 toggle @Test(groups = "Functional")
237    public void testColourByChain()
238    {
239  1 assertEquals(testee.colourByChain(),
240    new StructureCommand("spectrum", "chain"));
241    }
242   
 
243  1 toggle @Test(groups = "Functional")
244    public void testColourResidues()
245    {
246  1 assertEquals(testee.colourResidues("something", Color.MAGENTA),
247    new StructureCommand("color", "0xff00ff", "something"));
248    }
249   
 
250  1 toggle @Test(groups = "Functional")
251    public void testLoadFile()
252    {
253  1 assertEquals(testee.loadFile("/some/path"),
254    new StructureCommand("load", "/some/path"));
255    }
256   
 
257  1 toggle @Test(groups = "Functional")
258    public void testSetBackgroundColour()
259    {
260  1 assertEquals(testee.setBackgroundColour(Color.PINK),
261    new StructureCommand("bg_color", "0xffafaf"));
262    }
263   
 
264  1 toggle @Test(groups = "Functional")
265    public void testSetAttribute()
266    {
267  1 AtomSpecModel model = new AtomSpecModel();
268  1 model.addRange("1", 89, 92, "A");
269  1 model.addRange("2", 12, 20, "B");
270  1 model.addRange("2", 8, 9, "B");
271  1 assertEquals(testee.setAttribute("jv_kd", "27.3", model),
272    new StructureCommand("iterate", "1//A/89-92/ 2//B/8-9+12-20/",
273    "p.jv_kd='27.3'"));
274    }
275   
 
276  1 toggle @Test(groups = { "Functional" })
277    public void testSetAttributes()
278    {
279    /*
280    * make a map of { featureType, {featureValue, {residue range specification } } }
281    */
282  1 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
283  1 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
284   
285    /*
286    * start with just one feature/value...
287    */
288  1 featuresMap.put("chain", featureValues);
289  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
290   
291  1 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
292  1 assertEquals(commands.size(), 1);
293   
294    /*
295    * feature name gets a jv_ namespace prefix
296    */
297  1 assertEquals(commands.get(0), new StructureCommand("iterate",
298    "0//A/8-20/", "p.jv_chain='X'"));
299   
300    // add same feature value, overlapping range
301  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
302    // same feature value, contiguous range
303  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
304  1 commands = testee.setAttributes(featuresMap);
305  1 assertEquals(commands.size(), 1);
306  1 assertEquals(commands.get(0), new StructureCommand("iterate",
307    "0//A/3-25/", "p.jv_chain='X'"));
308   
309    // same feature value and model, different chain
310  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
311    // same feature value and chain, different model
312  1 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
313  1 commands = testee.setAttributes(featuresMap);
314  1 assertEquals(commands.size(), 1);
315  1 StructureCommand expected1 = new StructureCommand("iterate",
316    "0//A/3-25/ 0//B/21-25/ 1//A/26-30/", "p.jv_chain='X'");
317  1 assertEquals(commands.get(0), expected1);
318   
319    // same feature, different value
320  1 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
321  1 commands = testee.setAttributes(featuresMap);
322  1 assertEquals(2, commands.size());
323    // commands are ordered by feature type but not by value
324    // so test for the expected command in either order
325  1 StructureCommandI cmd1 = commands.get(0);
326  1 StructureCommandI cmd2 = commands.get(1);
327  1 StructureCommand expected2 = new StructureCommand("iterate",
328    "0//A/40-50/", "p.jv_chain='Y'");
329  1 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
330    // String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
331  1 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
332   
333  1 featuresMap.clear();
334  1 featureValues.clear();
335  1 featuresMap.put("side-chain binding!", featureValues);
336  1 ChimeraCommands.addAtomSpecRange(featureValues,
337    "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
338    // feature names are sanitised to change non-alphanumeric to underscore
339    // feature values are sanitised to encode single quote characters
340  1 commands = testee.setAttributes(featuresMap);
341  1 assertEquals(commands.size(), 1);
342  1 StructureCommandI expected3 = new StructureCommand("iterate",
343    "0//A/7-15/",
344    "p.jv_side_chain_binding_='<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!'");
345  1 assertEquals(commands.get(0), expected3);
346    }
347   
 
348  1 toggle @Test(groups = "Functional")
349    public void testCloseViewer()
350    {
351  1 assertEquals(testee.closeViewer(), new StructureCommand("quit"));
352    }
353    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 28 2024 18:14:23 GMT using coverage data from Thu Nov 28 2024 18:14:06 GMT.
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